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A Study of Functional Genomics for Unknown Proteins in Chlamydomonas reinhardtii

by Manisha D. Giripunje, Abhay B. Fulke, Pravin U. Meshram
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 81 - Number 10
Year of Publication: 2013
Authors: Manisha D. Giripunje, Abhay B. Fulke, Pravin U. Meshram
10.5120/14045-1710

Manisha D. Giripunje, Abhay B. Fulke, Pravin U. Meshram . A Study of Functional Genomics for Unknown Proteins in Chlamydomonas reinhardtii. International Journal of Computer Applications. 81, 10 ( November 2013), 1-6. DOI=10.5120/14045-1710

@article{ 10.5120/14045-1710,
author = { Manisha D. Giripunje, Abhay B. Fulke, Pravin U. Meshram },
title = { A Study of Functional Genomics for Unknown Proteins in Chlamydomonas reinhardtii },
journal = { International Journal of Computer Applications },
issue_date = { November 2013 },
volume = { 81 },
number = { 10 },
month = { November },
year = { 2013 },
issn = { 0975-8887 },
pages = { 1-6 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume81/number10/14045-1710/ },
doi = { 10.5120/14045-1710 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T21:55:41.276041+05:30
%A Manisha D. Giripunje
%A Abhay B. Fulke
%A Pravin U. Meshram
%T A Study of Functional Genomics for Unknown Proteins in Chlamydomonas reinhardtii
%J International Journal of Computer Applications
%@ 0975-8887
%V 81
%N 10
%P 1-6
%D 2013
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Chlamydomonas reinhardtii is a unicellular green alga, which has been used as a reference organism for identifying proteins. Five hundred hypothetical proteins in Chlamydomonas reinhardtii have been sequenced for knowing functions of the proteins in their families. Functions of Five hundred hypothetical proteins in Chlamydomonas reinhardtii were predicted using bioinformatics web tools. The web tools like CDD-BLAST, INTERPROSCAN and PFAM were used for the prediction of functions in the proteins by searching protein databases for the presence of conserved domains. The current study was useful in better knowing the functions of hypothetical proteins in Chlamydomonas reinhardtii and the various regulatory mechanisms, which interact to yield a final output from the system.

References
  1. Boesger, J. , Wagner, V. , Weisheit, W. , Mittag, M. 2009. Analysis of Flagellar Phosphoproteins from Chlamydomonas reinhardtii. Eukaryotic cell. 8(7), 922-932.
  2. Harris, E. 2001. Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol. 52, 363-406.
  3. Rochaix, J. , 1995. Chlamydomonas reinhardtii as the photosynthetic yeast. Annu. Rev. Genet. 29, 209-230.
  4. Merchant, S. , Prochnik, S. , Vallon, O. , Harris, E. , Karpowicz, S. , Witman, G. , et al. 2007. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245-250.
  5. Li, J. , 2004. Cell. 117, 541.
  6. Storms, R. , Hastings, P. 1977. Exp Cell Res. 104, 39.
  7. Merchant, S. , Allen, M, Kropat, J. , Moseley, J. , Long, J. , Tottey, S. , Terauchi, A. , 2006. Between a rock and a hard place: trace element nutrition in Chlamydomonas. Biochim Biophys Acta 1763, 578-594.
  8. Grossman, A. R. , Karpowicz, S. J. , Heinnickel, M. , Dewez, D. , Hamel, B. , Dent, R. , Niyogi, K. K. , Johnson, X. , Alric, J. , Wollman, F. A. , Li, H. , Merchant, S. S. 2010. Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynth Res. 106, 3-17.
  9. Gore, D. 2009. In silico Prediction of Structure and Enzymatic Activity for Hypothetical Proteins of Shigella flexneri. Biofrontiers. 1(2), 1-10.
  10. Edward, E. , Gary, L. G. , Osnat, H. , John, M. , John, O. , Roberto, J. P. , Linda, B. , Delwood, R. , Andrew, J. H. 2000. Biological function made crystal clear- annotation of hypothetical proteins via structural genomics. Current Opinion in Biotechnology. 11, 25-30.
  11. Choi, E. J. , Bae, S. M. , Ahn, W. S. 2008. Antiproliferative effects of quercetin through cell cycle arrest and apoptosis in human breast cancer MDA-MB-453 cells. Arch Pharm Res.
  12. Altschul, S. F. , Madden, T. L. , Schaffer, A. A. , Zhang, J. , Zhang, Z. , Miller, W. , Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: "a new generation of protein database search programs". Nucleic Acids Res. 25 (17), 3389-402.
  13. Schaffer, A. A. , Aravind, L. , Madden, T. L. , Shavirin, S. , Spouge, J. L. , Wolf, Y. I. , Koonin, E. V. , Altschul, S. F. 2001. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14), 2994-3005.
  14. Aron, M. , Bauer, John, B. A. , Myra, K, D. , Carol, D. S. , Noreen, R. G. , Marc, G. , Luning, H. , Siqian, H. , David, I. H. , John, D. J. , Zhaoxi, K. , Dmitri, K. , Christopher, J. L. , Cynthia, A. L. , Chunlei, L. , Fu, L. , Shennan, L. , Gabriele, H. M. , Mikhail, M. , James, S. S. , Narmada, T. , Roxanne, A. Y. , Jodie, J. Y. , Dachuan, Z. , Stephen, H. B. 2006. CDD: "a conserved domain database for interactive domain family analysis. "Nucleic Acids Research. 35, 237-240.
  15. Marchler-Bauer, A. 2011. Nucleic Acids Res. 39, 225.
  16. Zdobnov, E. M. , Rolf, A. 2001. Interproscan- an integration platform for the signatures recognition methods in InterPro. Bioinformatics . 17, 847-848.
  17. Alex, B. , Lachlan, C. , Richard, D. , Robert, D. F. , Volker, H. , Sam, G. J. , Ajay, K. , Mhairi, M. , Simon, M. , Erik, L. L. S. , David, J. S. , Corin, Y. , Sean, R. E. 2004. The Pfam families' database. Nucleic Acids Research. 32, 138-141.
  18. Finn, R. D. 2010. Nucleic Acids Res. 38, 211.
  19. Grossman, A. R. , Steven, J. , Karpowicz, M. , Heinnickel, D. , Dewez, B. , Hamel, R. , Dent, T. , Niyogi, K. K. 2010. Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynthesis research 106, 3-17.
  20. Misra, N. , Panda P. K. , Parida B. K. , Mishra B. K. 2012. Phylogenomic Study of Lipid Genes Involved in Microalgal Biofuel Production—Candidate Gene Mining and Metabolic Pathway Analyses. Evolutionary bioinformatics online 8, 545.
Index Terms

Computer Science
Information Sciences

Keywords

Chlamydomonas reinhardtii Bioinformatics Web Tools hypothetical proteins Conserved Domains

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